Unlike your other HTML pages, the pdf link doesn't contain GA tracking code and that is the reason why it is not being tracked by Google Analytics. To tackle this problem, you can follow this approach:
Edit the link to the pdf so that it looks something like:
< a href="http://site.com/trackpdf.pdf" onclick="gaq.push(['trackPageview', '/mypdfs/trackpdf.pdf']);" target="_blank">PDF< /a>
Let me know if you still face an issue.